Well, I've always thought that Snape was the one of the 3 missing death eaters. There's Moody/Crouch, Karkaroff, and Snape. Voldie's just bidding his time until he kills Snape. He's known from the beginning and has a sinister little plan for him. Of course, Snape might not be spying at all. Maybe he lied about it to Harry. After all, would you be truthful about sensitive matter like that with a boy who has a direct telephone line with Lord Voldemort? I wouldn't.
Still, I go with my first theory. Anyway, I doubt polyjuice potion is a factor---especially turning into Crouch. Voldemort is well connected enough to know that he died. Malfoy has Fudge, who was present at the kiss, in his pocket. Remember?